Help building a square box under my complex 3D model!
The following approach gives you an object with the river bed on the bottom side and a volume with planar surface.



First load the model of the riverbed, then switch to edit mode and select all vertices A.



Then extrude the surface either with the extrude tool on the left hand side or by pressing E. Then move the mouse cursor upwards so that the model is a bit taller then the desired end result.



The following steps depend on whether you want to modify only the Z-direction or if you want intersect the entire model with another volume.

If you just want to modify the Z-direction press S, Z and 0 with the extruded part still selected. This will scale the Z-direction to zero making it completely flat. You may have to adjust the Z position to the desired height by pressing G and Z. Then you should be done, unless you want to flip the normals which is described in the last step below.

If you'd like to intersect the model with a cubic volume you need to do the following steps.

Next add a Cube in object mode and scale it so the desired section of the riverbed is inside the volume. The height of the Cube should be the height you want the final model to have.



Now apply a Boolean modifier to the Cube.



Set the Operation to Intersection  and set the object to your riverbed model.



Now you can remove or hide the other model and just keep the result of the boolean operation. If you need the normals to face inwards for the simulation you can switch to the edit mode and recalculate the normals inside (Mesh > Normals > Recalculate Inside) or SHIFT+CTRL+N.